ToolUniverse is a collection of tools, interfaces, and supporting components for building AI systems that perform scientific work. It is for developers creating AI scientist agents that use APIs, databases, machine-learning tools, and domain-specific utilities. The catalogue includes skills, commands, an MCP server, an agent, and a hook for working with the ecosystem.
Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add mims-harvard/ToolUniverse --skill tooluniverse-organic-chemistrygit clone --depth 1 https://github.com/mims-harvard/ToolUniverseWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/mims-harvard/tooluniverse/tooluniverse-organic-chemistry)<a href="https://agentmods.dev/skills/mims-harvard/tooluniverse/tooluniverse-organic-chemistry"><img src="https://agentmods.dev/badge/skills/mims-harvard/tooluniverse/tooluniverse-organic-chemistry/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/mims-harvard/tooluniverse/tooluniverse-organic-chemistry"><img src="https://agentmods.dev/badge/skills/mims-harvard/tooluniverse/tooluniverse-organic-chemistry.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- NVIDIA SkillSpector pass
What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00086 | $0.05528 |
| Opus 5 | $0.00043 | $0.02764 |
| Sonnet 5 | $0.00017 | $0.01106 |
| Haiku 4.5 | $0.00009 | $0.00553 |
Grade A, and why
tooluniverse-organic-chemistry scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 8d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
How it starts
The opening of the file, as written. The whole thing — 346 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Organic Chemistry Reasoning Guide
This skill teaches how to think through organic chemistry problems, not what to memorize.
1. Predicting Reaction Products — A Reasoning Process
Do NOT pattern-match to a named reaction. Instead, reason from first principles:
Step 1 — Find the most reactive sites
Look at each molecule and ask: where is the electron density?
- Electron-rich sites (nucleophiles): lone pairs on N, O, S; pi bonds (C=C, aromatics); carbanions; enolates
- Electron-poor sites (electrophiles): carbons bonded to electronegative atoms (C=O, C-X); carbocations; atoms with empty orbitals
The reaction will happen where the strongest nucleophile meets the strongest electrophile.
Step 2 — What kind of bond-making/breaking is this?
Three fundamental categories:
- Ionic (polar): electrons move in pairs. One species donates electrons, the other accepts. Most common in solution chemistry.
- Radical: electrons move one at a time. Look for: heat + peroxides, UV light (hv), NBS, or radical initiators.
- Pericyclic: electrons move in a concerted cyclic transition state. Look for: heat or light with no other reagents, dienes + dienophiles, sigmatropic rearrangements.
Step 3 — Where do the electrons flow?
Draw the arrow from nucleophile to electrophile. Ask:
- Which atom has the best orbital overlap?
- Is backside attack required (SN2) or can the nucleophile approach from either face (SN1)?
- For additions to C=C: which carbon gets the electrophile? (Markovnikov = more substituted carbocation intermediate; anti-Markovnikov = radical or hydroboration)
- For additions to C=O: the nucleophile attacks carbon (Burgi-Dunitz angle ~107 degrees).
- For E2 eliminations: base size determines regiochemistry. Bulky bases (KOtBu, LDA, DBU) favor the Hofmann product (less substituted alkene) because they abstract the less sterically hindered proton. Small bases (NaOEt, KOH, NaOMe) favor the Zaitsev product (more substituted, more stable alkene). Always check base size before predicting regiochemistry.
- For ion tracking in multi-step syntheses: write out the complete ionic equation at each step. Track every cation and anion through each transformation — identify what dissolves, what precipitates, what complexes form, and what remains in solution. Verify at each step: are all ions accounted for? Does the mass balance? Use solubility rules (Ksp) and complex stability constants (Kf) to predict which species persist.
What ships with it
7 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
- scripts/chemistry_facts.py 46 KB runs code
- scripts/crystal_validator.py 7.5 KB runs code
- scripts/degrees_of_unsaturation.py 7.3 KB runs code
- scripts/molecular_complexity.py 4.8 KB runs code
- scripts/molecular_formula.py 11 KB runs code
- scripts/smiles_verifier.py 16 KB runs code
- scripts/stereochem_tracker.py 8.4 KB runs code
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 8d ago First seen · 346 lines · 86 tokens per session scan A 8226c306b90e
tooluniverse-organic-chemistry is a skill published in the GitHub repository mims-harvard/ToolUniverse (1,680 stars, last pushed 3d ago), licensed Apache-2.0. It adds 86 tokens to every session and 5,528 once invoked, about $0.0004 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-03.
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